phy is an open-source Python library providing a graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites (mostly Neuropixels probes).
Phy provides two GUIs:
It is recommanded to store the data on a SSD for performance reasons.
There are no specific GPU requirements as long as relatively recent graphics and OpenGL drivers are installed on the system.
Installation instructionsRun the following commands in a terminal:
Create a new conda environment with the conda dependencies:
conda create -n phy2 -y cython dask h5py joblib matplotlib numpy pillow pip pyopengl pyqt pyqtwebengine pytest python qtconsole requests responses scikit-learn scipy traitlets
Activate the new conda environment with conda activate phy2
Install the development version of phy: pip install git+https://github.com/cortex-lab/phy.git
[OPTIONAL] If you plan to use the Kwik GUI, type pip install klusta klustakwik2
Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):
cd path/to/my/spikesorting/output phy template-gui params.pyDealing with the error
ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidget
In some environments, you might get an error message related to QtWebEngineWidget. Run the command pip install PyQtWebEngine and try launching phy again. This command should not run if the error message doesn't appear, as it could break the PyQt5 installation.
~/.phy/*GUI/state.json when upgrading.To install the development version of phy in a fresh environment, do:
git clone git@github.com:cortex-lab/phy.git cd phy pip install -r requirements.txt pip install -r requirements-dev.txt pip install -e . cd .. git clone git@github.com:cortex-lab/phylib.git cd phylib pip install -e . --upgradeRunning phy from a Python script
In addition to launching phy from the terminal with the phy command, you can also launch it from a Python script or an IPython terminal. This may be useful when debugging or profiling. Here's a code example to copy-paste in a new launch.py text file within your data directory:
from phy.apps.template import template_gui
template_gui("params.py")
phy is developed and maintained by Cyrille Rossant.
Contributors to the repository are:
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